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Updating molecular diagnosis to ever-changing PRRS virus

Updating molecular diagnosis to ever-changing PRRS virus

The changing nature of PRRS virus, partly due to its unstable genome, requires constant updating of the detection methods in the laboratory. Currently, molecular methods such as the PCR and those emerging technologies based on the analysis of the viral genome are turning increasingly to the study of the PRRS virus evolution, and virus adaptation to the equally changing conditions of the pig farm environment.

Since the emergence of the porcine reproductive and respiratory syndrome (PRRS), the diagnosis of this infectious disease in the laboratory has been a key component in the control of the disease, in an attempt to reduce its negative effects on pig production. However, it is well known that viruses whose genome is composed of RNA present greater instability than those containing DNA. This inherent characteristic of the PRRS virus has become a real challenge for the global swine industry.

The polymerase chain reaction (PCR) used for the detection of PRRS virus is based on the identification of short sequences (100-500 nucleotides) located in two or three genes of the viral genome. If mutations occur in those areas that are recognized by the PCR, no recognition will occur, and false negative results will be obtained in the assay. This drawback is overcome partially by modifying the design of the PCR, in an attempt to adapt it to the strains of PRRS virus circulating in each region. That may be done periodically with in-house PCR methods that can be modified in the laboratory. However, there are numerous commercial PCR kits specifically designed for the detection and differentiation of certain genotypes of PRRS virus.

These kits are an affordable alternative for the detection of PRRS virus in laboratories that do not have the capacity to develop and update their own methods. However, commercial kits cannot be updated with the same speed as the in-house methods, and their sensitivity is affected by the emergence of variant strains, or if they are used in regions of the world where circulating viruses are genetically different from those used to design the commercial kit. A recent study dealing with a comparative study of diverse kits and in-house PCR methods concludes that a good strategy to detect the PRRS virus by using PCR is to use first a generic PCR method based on highly conserved segments of the viral genome allowing detection with high sensitivity, followed by partial sequencing.

Partial or complete sequencing of PRRSV genome aims characterization of field virus with epidemiological purposes. However, knowledge of the dynamics of infection of domestic strains at herd level, or the detection of exotic strains of PRRS virus that have infected a population of pigs lacking immunity to that new strain, are also situations in which sequencing can help in decision making. The New Generation Sequencing (NGS) is a research technology that is breaking into the clinical setting for diagnosis. This sequencing system promises to solve some of the limitations of conventional sequencing, as it does not depend of a previous PCR for detection, it can be applied directly to the infected animal tissues, allows obtaining sequences with minimal error, and covers almost the entire genome of the virus instead of small portions within particular genes.

A recent study has demonstrated the usefulness of the NGS in the characterization of field and vaccine strains of PRRS virus. The strains detected in various farms in Hong Kong showed a never before described genetic diversity, whose exact meaning is not possible to assess, but helps to understand a little more the ever changing nature of PRRS virus. With lowering of the cost of machines and reagents used for the NGS, and the availability of commercial platforms, the NGS will certainly be a routine system for the diagnosis of infectious diseases caused by viruses in human and veterinary medicine.